Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008788.1 Corchorus capsularis cultivar CVL-1 contig08809, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 6227
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:693 original size:30 final size:30

Alignment explanation


    Indices: 659--720  Score: 97
    Period size: 30  Copynumber: 2.1  Consensus size: 30

        649 TCGGTAAGAA

                            * *           
        659 AAACGACAGAGGAAACGATGGCAACGCTTC
          1 AAACGACAGAGGAAACAACGGCAACGCTTC

                 *                        
        689 AAACGGCAGAGGAAACAACGGCAACGCTTC
          1 AAACGACAGAGGAAACAACGGCAACGCTTC

              
        719 AA
          1 AA

        721 TTCTCGGCCA


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.42, C:0.24, G:0.26, T:0.08


Consensus pattern (30 bp):   
AAACGACAGAGGAAACAACGGCAACGCTTC

Found at i:1516 original size:29 final size:30

Alignment explanation


    Indices: 1457--1521  Score: 75
    Period size: 29  Copynumber: 2.3  Consensus size: 30

       1447 ACTATTTTTG

                          *               
       1457 TTTATTA--TAAATCTTTATTGTTAATTAT
          1 TTTATTATGTAAATATTTATTGTTAATTAT

                                         * 
       1485 TTT-TTATGTAAATATTTATT-TTAACTTCT
          1 TTTATTATGTAAATATTTATTGTTAA-TTAT

                    
       1514 TTTATTAT
          1 TTTATTAT

       1522 TATTATTTAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 6
        0.79            0.05        0.15

Matches are distributed among these distances:
  27    3  0.10
  28    7  0.23
  29   17  0.55
  30    4  0.13

ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63


Consensus pattern (30 bp):   
TTTATTATGTAAATATTTATTGTTAATTAT

Found at i:2203 original size:1 final size:1

Alignment explanation


    Indices: 2197--2225  Score: 58
    Period size: 1  Copynumber: 29.0  Consensus size: 1

       2187 AAAATTGCCG

                                         
       2197 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       2226 TCTCAACCGA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   28  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:5165 original size:85 final size:85

Alignment explanation


    Indices: 5067--5232  Score: 305
    Period size: 85  Copynumber: 2.0  Consensus size: 85

       5057 TAAAATTTTT

                                         *                         *         
       5067 TTTTGTTTGGGTTTCATATATTCTTTTTAGTTAATTTCATTCAATATAATTTGTAGCAAATGCAA
          1 TTTTGTTTGGGTTTCATATATTCTTTTTAATTAATTTCATTCAATATAATTTGTAACAAATGCAA

                                
       5132 TCTCTAAATTTAACAATTTG
         66 TCTCTAAATTTAACAATTTG

                                                 *                           
       5152 TTTTGTTTGGGTTTCATATATTCTTTTTAATTAATTTTATTCAATATAATTTGTAACAAATGCAA
          1 TTTTGTTTGGGTTTCATATATTCTTTTTAATTAATTTCATTCAATATAATTTGTAACAAATGCAA

                            
       5217 TCTCTAAATTTAACAA
         66 TCTCTAAATTTAACAA

       5233 ATATCCGAGA


Statistics
Matches: 78,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  85   78  1.00

ACGTcount: A:0.31, C:0.10, G:0.09, T:0.49


Consensus pattern (85 bp):   
TTTTGTTTGGGTTTCATATATTCTTTTTAATTAATTTCATTCAATATAATTTGTAACAAATGCAA
TCTCTAAATTTAACAATTTG

Found at i:5726 original size:22 final size:21

Alignment explanation


    Indices: 5698--5770  Score: 87
    Period size: 22  Copynumber: 3.5  Consensus size: 21

       5688 TCTCTGTATA

                                 *
       5698 GTTATCAAAATTTCATAATGAG
          1 GTTATCAAAATTTCATAA-GAT

                                 
       5720 GTTATCAAAATTTCAT-AG-T
          1 GTTATCAAAATTTCATAAGAT

              *               *   
       5739 GTGATCAAAATTTCATAGCGAT
          1 GTTATCAAAATTTCATA-AGAT

                      
       5761 GTTATCAAAA
          1 GTTATCAAAA

       5771 GGCCTAATGT


Statistics
Matches: 44,  Mismatches: 4, Indels: 6
        0.81            0.07        0.11

Matches are distributed among these distances:
  19   15  0.34
  20    1  0.02
  21    2  0.05
  22   26  0.59

ACGTcount: A:0.40, C:0.11, G:0.14, T:0.36


Consensus pattern (21 bp):   
GTTATCAAAATTTCATAAGAT
Done.